Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA.

Genetics
Naoko Takezaki, Masatoshi Nei

Abstract

Microsatellite DNA loci or short tandem repeats (STRs) are abundant in eukaryotic genomes and are often used for constructing phylogenetic trees of closely related populations or species. These phylogenetic trees are usually constructed by using some genetic distance measure based on allele frequency data, and there are many distance measures that have been proposed for this purpose. In the past the efficiencies of these distance measures in constructing phylogenetic trees have been studied mathematically or by computer simulations. Recently, however, allele frequencies of 783 STR loci have been compiled from various human populations. We have therefore used these empirical data to investigate the relative efficiencies of different distance measures in constructing phylogenetic trees. The results showed that (1) the probability of obtaining the correct branching pattern of a tree (PC) is generally highest for DA distance; (2) FST*, standard genetic distance (DS), and FST/(1-FST) give similar PC-values, FST* being slightly better than the other two; and (3) (deltamu)2 shows PC-values much lower than the other distance measures. To have reasonably high PC-values for trees similar to ours, at least 30 loci with a minimum of 15 ind...Continue Reading

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Citations

Dec 15, 2010·Tropical Animal Health and Production·Nedup DorjiYupin Phasuk
Jan 21, 2009·The Journal of Heredity·Lori S EggertRobert C Fleischer
May 2, 2009·Molecular Biology and Evolution·Naoko Takezaki, Masatoshi Nei
Sep 22, 2009·Canadian Journal of Microbiology·André Pitondo-SilvaAna Lúcia C Darini
Dec 18, 2009·BMC Genomics·Trevor J PembertonNoah A Rosenberg
Dec 17, 2014·Molecular Ecology·Dietrich GotzekDeWayne Shoemaker
Jul 25, 2009·Molecular Ecology·Jean-François ArnaudJoël Cuguen
May 13, 2009·Annals of the New York Academy of Sciences·Craig R Primmer
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Aug 7, 2013·Ecology and Evolution·Kaela B BeauclercAlbrecht I Schulte-Hostedde
Apr 10, 2007·BMC Genetics·Faisal KhanSuraksha Agrawal
Oct 29, 2009·BMC Evolutionary Biology·Cristiane C ThompsonFabiano L Thompson
Dec 11, 2008·PLoS Biology·Elizabeth A OstrowskiJoan E Strassmann
Nov 13, 2010·PLoS Neglected Tropical Diseases·Aurélien MercierMarie-Laure Dardé
Jun 15, 2011·PLoS Neglected Tropical Diseases·Bashir SalimChihiro Sugimoto
Nov 28, 2007·PLoS Genetics·Sijia WangAndrés Ruiz-Linares
Apr 26, 2011·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Jacques KaboréThierry De Meeûs
Nov 27, 2002·Molecular Phylogenetics and Evolution·Trinidad PérezAna Domínguez
May 3, 2011·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Jacques KaboréVincent Jamonneau

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